Africa is the geographic origin of anatomically modern humans; it is also home to a third of all modern languages, including four major language families: Niger-Kordofanian, Afro-Asiatic, Nilo-Saharan, and Khoesan. Despite the importance of African populations for studying human origins and the complexity of demographic and linguistic relationships among African populations, genome-wide analyses of sub-Saharan variation have been sparse. To address this deficiency, we used Illumina 1M-Duo SNP arrays to genotype samples (N=697) from 44 sub-Saharan populations, which we supplemented with published data sets. Principal components analysis (PCA) and linear regression were used to assess the statistical effect of geography and linguistics on the partitioning of genetic variation. As ascertainment bias can distort the allele frequency spectrum, we examined patterns of linkage disequilibrium (LD), haplotype sharing, and identity by descent (IBD) to understand the demographic relationship among populations. To affirm that LD-based analyses were robust to ascertainment bias, we assessed the rank correlation of estimates of effective population size from the rate of LD decay within populations and estimates of population size based on the variance of microsatellite repeat lengths from previously published data (Spearman’s ρ=0.782, p=0.011). Additionally, the presence of long IBD tracts between individuals indicates recent common ancestry. Thus, we used the GERMLINE algorithm to infer IBD tracts between individuals in hunting-gathering populations and neighboring agriculturalist and pastoralist populations. To infer the time to most recent common ancestor and test demographic models while accounting for the confounding effects of migration and changes in population sizes, we employed Approximate Bayesian Computation (ABC) using summaries of haplotype frequency, diversity and sharing within and between populations. We report, for the first time, evidence for recent common ancestry of Ethiopian hunter-gatherers and the Kenyan Sanye/Dahalo, who speak a language with remnant clicks, with click-speaking eastern African Khoesan populations. This work supports archaeological and linguistic studies that indicate that the distribution of Khoesan speaking populations may have extended as far north as Ethiopia.

Not very surprising to me, as I detected a contribution of the "Palaeo_African" component (which has one of its peaks in San) in East Africans.

Comparative study of the Y chromosome diversity in some ethnic groups living in Iran and populations of the Middle East.

L. Andonian et al.

Background: The main goal of this study is to conduct a population genetic study of: a) Armenians living in Iran, in the context of general Armenian population; and b) Iranian Azeris, one of the biggest ethno-linguistic communities, in comparison with other Turkic-speaking populations of the Middle East (from eastern Turkey, Azerbaijan Republic and Turkmenistan). Methods: Buccal cells of 89 Armenian males from central Iran, the descendants of Armenians forcibly moved to Iran in the beginning of 17th century CE, and 105 Turkic-speaking Azeri males from north-west Iran (Tabriz) were collected by mouth swabs. The samples were screened for 12 Single Nucleotide (SNP) and 6 microsatellite markers on the non-recombining portion of the Y chromosome. The results of genetic typing were statistically analyzed using Arlequin software. Results: Iranian Armenians display a moderate level of genetic variation and are genetically closer to Western Armenians which is in agreement with historical records. Iranian Azeris demonstrate much weaker genetic resemblance with Turkmens (as putative source population) than with their geographic neighbors. Conclusion: Political, religious and geographic isolation had moderate influence on the genetic structure of modern Iranian Armenians during the last four centuries, which is expressed in lower diversity of their patrilineal genetic legacy. The imposition of Turkic language to the populations of north-west Iran was realized predominantly by the process of elite dominance,i.e. by the limited number of invaders who left weak traces in the patrilineal genetic history of Iranian Azeris.

A direct characterization of human mutation.

J. X. Sun et al.

Mutation and recombination provide the raw material of evolution. This study reports the largest study of new mutations to date: 2,058 germline mutations discovered by analyzing 85,289 Icelanders at 2,477 microsatellites. We find that the paternal-to-maternal mutation rate ratio is 3.3, and that the mutation rate in fathers doubles between the ages of 15 to 45 whereas there is no association to age in mothers. Strong length constraints apply for microsatellites, with longer alleles tending to mutate more often and decrease in length, whereas shorter alleles tending to mutate less often and increase in length. Based on these direct observations of the microsatellite mutation process, we build a model to estimate key parameters of evolution without calibration to the fossil record. The sequence substitution rate per base pair is estimated to be 1.84-2.21×10-8 per generation (95% credible interval). Human-chimpanzee speciation is estimated to be 3.92-5.91 Mya, challenging views of the Toumaï fossil as dating to >6.8 Mya and being on the hominin lineage since the final separation of humans and chimpanzees.

This microsatellite based estimate of human-chimp speciation contrasts with a recent SNP-based estimate of 7 million years.

Genetic structure of Jewish populations on the basis of genome-wide single nucleotide polymorphisms.

N. M. Kopelman

The Jewish population forms a genetically structured population, due to historical migrations and diverse histories of the various Jewish communities. Discerning the ancestry and population structure of different Jewish populations is important for understanding the complex history of the Jewish communities as well as for research on the genetic basis of disease. Using >500,000 genome-wide single-nucleotide polymorphisms, we investigated patterns of population structure in 438 samples from 30 Jewish populations in the context of additional samples from non-Jewish populations. The collection of Jewish populations studied incorporates a variety of populations not previously included in other genomic population structure studies of Jewish groups (e.g. NM Kopelman et al. 2009 BMC Genet 10:80; G Atzmon et al. 2010 AJHG 86:850-859; DM Behar et al. 2010 Nature 466:238-242; SM Bray et al. 2010 PNAS 107:16222-16227; JB Listman et al. 2010 BMC Genet 11:48). We identify fine-scale population structure within the Jewish samples, including notable distinctions separating Ashkenazi, Mizrahi, Sephardi, and North African populations. Additionally, we identify distinctions within major regional groups, including a separation among the North African populations of Libyan, Moroccan, and Tunisian Jewish samples and a separation among the Mizrahi populations of Bukharan, Georgian, Iranian, and Iraqi Jewish samples. These results supply enhanced information regarding Jewish population structure, providing a basis for further detailed analysis of the genetic history of Jewish populations.

Hopefully the wealth of this new Jewish and non-Jewish data will be made publicly available.

LD patterns in dense variation data reveal information about the history of human populations worldwide.

S. Myers et al.

A detailed understanding of population structure in genetic data is vital in many applications, including population genetic analyses and disease gene mapping, and relates directly to human history. However, there are still few methods that directly utilize information contained in the haplotypic structure of modern dense, genome-wide variation datasets. We have developed a set of new approaches, founded on a model first introduced by Li and Stephens, which fully use this powerful information, and are able to identify the underlying structure in large datasets sampling 50 or more populations. Our methods utilize both Bayesian model-based clustering and principal component analyses, and by using LD information effectively, consistently outperform existing approaches in both simulated and real data. This allows us to infer ancestry with unprecedented geographical precision, in turn enabling us to characterize the populations involved in ancient admixture events and, critically, to precisely date such events. We applied our new techniques to combined data for 30 European populations sampled by us, or publicly available, and the worldwide HGDP data. We find almost all human populations have been influenced by mixture with other groups, with the Bantu expansion, the Mongol empire and the Arab slave trade leaving particularly widespread genetic signatures, and many more local events, for example North African (Moroccan) admixture into the Spanish that we date to 834-1394AD. Dates of admixture events between European groups and groups from North Africa and the Middle East, seen in multiple Mediterranean countries, vary between 800 and 1700 years ago, while Greece, Croatia and other Balkan states show signals of admixture consistent with Slavic migration from the north, which we date to 600-1000AD. At the finest scale, we are able to study admixture patterns in data gathered by a project (POBI) examining people within the British Isles. Our approaches reveal genetic differences between individuals from different UK counties, and show that the current UK genetic landscape was formed by a series of events in the millennium following the fall of the Roman Empire.

Existing methods (see comments below) for dating historical admixture events differ from each other by a factor of two, and they all assume a 2-population model. Hopefully the research described here will be an improvement, especially if it is encapsulated in an easy-to-use piece of software. It will definitely be interesting to see the evidence for Slavic admixture in the Balkans, which probably corresponds somewhat to the "East European" component discovered in the Dodecad Project which differentiates Balkan populations from their Italian and West Asian neighbors.

Evidence for extensive ancient admixture in different human populations.

J. Wall et al.

We generated whole-genome sequences from four Biaka pygmies and analyzed them along with the publicly available genomes of 69 individuals from a range of different ethnicities. We scanned each of the 73 genomes for regions with unusual patterns of genetic variation that might have arisen due to ancient admixture with an ‘archaic’ human group. While a majority of the most extreme regions were really misalignment errors, we did find hundreds of regions that likely introgressed in from archaic human ancestors, and we estimate the amount and the timing of these ancient admixture events. These regions were found in the genomes of both sub-Saharan African and non-African populations. While Neandertals are a natural source population for ancient admixture into non-Africans, the source for ancient admixture into sub-Saharan African populations is less obvious.

Wall and Hammer have been arguing for archaic admixture foryears, and there's a good chance they finally found the "smoking gun" here. I've argued before that Homo sapiens was not the only species in Africa at the time of its emergence, due to the great ecological diversity of the continent, and the long adaptation of humans there. We are unlikely to ever be able to find and sequence Paleolithic non-sapiens Homo from tropical Africa, but the signal is there to be discovered in modern African hunter-gatherers.

Validating the authenticity of the pedigrees of Chinese Emperor CAO Cao of 1,800 years ago.

H. Li

Deep pedigrees are of great value for studying the Y chromosome evolution. However, the authenticity of the pedigree information requires careful validation. Here, we validated some deep pedigrees in China with full records of 70-100 generations spanning over 1,800 years by comparing their Y chromosomes. The present clans of these pedigrees claim to be descendants of Emperor CAO Cao (155AD-220AD). Haplogroup O2-M268 is the only one that is enriched significantly in the claimed clans (P=9.323×10-5, OR=12.72), and therefore, is most likely to be that of the Emperor. Moreover, our analysis showed that the Y chromosome haplogroup of the Emperor is different from that of his claimed ancestry of the earlier CAO aristocrats (Haplogroup O3-002611). This study offers a successful showcase of the utility of genetics in studying the ancient history.

This is probably the oldest attested Y-chromosome lineage currently available. Confucius next? It will be interesting to know how many likely Cao descendants there are today, as a control on the rate with which a socially-selected lineage can grow.

Exceptions to the "One Drop Rule"? DNA evidence of African ancestry in European Americans.

J. L. Mountain et al.

Genetic studies have revealed that most African Americans trace the majority (75-80%, on average) of their ancestry to western Africa. Most of the remaining ancestry traces to Europe, and paternal lines trace to Europe more often than maternal lines. This genetic pattern is consistent with the "One Drop Rule,” a social history wherein children born with at least one ancestor of African descent were considered Black in the United States. The question of how many European Americans have DNA evidence of African ancestry has been studied far less. We examined genetic ancestry for over 77,000 customers of 23andMe who had consented to participate in research. Most live in the United States. A subset of about 60,000 shows genetic evidence of fewer than one in 16 great-great-grandparents tracing ancestry to a continental region other than Europe. They are likely to consider themselves to be entirely of European descent. We conducted two analyses to understand what fraction of this group has genetic evidence of some ancestry tracing recently to Africa. We first identified individuals whose autosomal DNA indicates that they are predominantly of European ancestry, but who carry either a mitochondrial (mt) DNA or Y chromosome haplogroup that is highly likely to have originated in sub-Saharan Africa. Of the 60,000 individuals with 95% or greater European ancestry, close to 1% carry an mtDNA haplogroup indicating African ancestry. Of approximately 33,000 males, about one in 300 trace their paternal line to Africa. We then identified the subset of these European Americans who have estimates of between 0.5% and 5.0% of ancestry tracing to Africa. This subset constitutes about 2% of this set of individuals likely to be aware only of their European ancestry. The majority (75%) of that group has a very small estimated fraction of African ancestry (about 0.5%), likely to reflect African ancestry over seven generations (about 200 years) ago. We estimate that, overall, at least 2-3% of individuals with predominantly European ancestry have genetic patterns suggesting relatively deep ancestry tracing to Africa. This fraction is far lower than the genetic estimates of European ancestry of African Americans, consistent with the social history of the United States, but reveals that a small percentage of “mixed race” individuals were integrating into the European American community (passing for White) over 200 years ago, during the era of slavery in the United States.

Hopefully this was not done with 23andMe's "Ancestry Painting" that grossly overestimates European ancestry with even East Africans and South Asians often getting >90% "European". The search for non-white ancestry seems to be a favorite pastime of many people who test at 23andMe, so this could potentially bias the results; on the other hand, I've encountered many, many more people who are seeking that illusive Amerindian ancestor of family lore, so, perhaps this is not as big of a problem for the detection of African ancestry.

Estimating a date of mixture of ancestral South Asian populations.

P. Moorjani

Linguistic and genetic studies have shown that most Indian groups have ancestry from two genetically divergent populations, Ancestral North Indians (ANI) and Ancestral South Indians (ASI). However, the date of mixture still remains unknown. We analyze genome-wide data from about 60 South Asian groups using a newly developed method that utilizes information related to admixture linkage disequilibrium to estimate mixture dates. Our analyses suggest that major ANI-ASI mixture occurred in the ancestors of both northern and southern Indians 1,200-3,500 years ago, overlapping the time when Indo-European languages first began to be spoken in the subcontinent. These results suggest that this formative period of Indian history was accompanied by mixtures between two highly diverged populations, although our results do not rule other, older ANI-ASI admixture events. A cultural shift subsequently led to widespread endogamy, which decreased the rate of additional population mixtures.

I have previously highlighted that ROLLOFF, the method used by these authors produces age estimates that are about half the age of HAPMIX and StepPCO. As of this writing, ROLLOFF does not seem to be available for independent evaluation, so it is not entirely clear to me whether it, or the older methods, are right. It would be great if this issue is dealt with in the publication arising from this research.

Another issue that must be dealt with is the spurious inference that Ancestral North Indians are more closely related to Europeans than to West Asians in the previous publication on the ANI/ASI division, an inference that was an artifact of unequal sample sizes between Adygei and CEU.

Synthesis of autosomal and gender-specific genetic structures of the Uralic-speaking populations.

K. Tambets et al.

The variation of uniparentally inherited genetic markers - mitochondrial DNA (mtDNA) and non-recombining part of Y chromosome (NRY) - has suggested somewhat different demographic scenarios for the spread of maternal and paternal lineages of North Eurasians, in particular those speaking Uralic languages. The west-east-directed geographical component has evidently been the most important factor that has influenced the proportion of western and eastern Eurasian mtDNA types among Uralic-speakers. The palette of maternal lineages of Uralic-speakers resemble that of geographically close to them European or Western Siberian Indo-European and Altaic-speaking neighbours. However, the most frequent in North Eurasia NRY type N1c, that is a common patrilineal link between almost all Uralic-speakers of eastern and western side of the Ural Mountains, is rare among Indo-European-speakers, with a notable exception of Latvians, Lithuanians and North Russians. In this study the information of genetic variation of uniparentally inherited markers in Uralic-speaking populations from 13 Finno-Ugric and 3 Samoyedic speakers is combined with the results of their genome-wide analysis of 650 000 SNPs (Illumina Inc.) to assign their place in a landscape of autosomal variation of North Eurasian populations and globally. The genome-wide analysis of the genetic profiles of studied populations showed that the proportion between western and eastern ancestry components of Uralic-speakers is concordant with their mtDNA data and is determined mostly by geographical factors. Interestingly, among the Saami - the population which is often considered as a genetic outlier in Europe - the dominant western component is accompanied by about one third of the eastern component, making the Saami genetically more similar to Volga-Finnic populations than to their closest Fennoscandian-East Baltic neighbors. The high frequency of pan-northern-Eurasian paternal lineage N1c among Saami cannot explain this phenomenon alone - genetic ancestry profiles of autosomes of other Finnic- and Baltic-speaking populations, who share the high N1c with the Saami, do not show a considerable eastern Asian contribution to their genetic makeup.

This study seems to include more Northern Eurasian references, but we will have to wait and see how its components are defined. Notice the slight discrepancy between its eastern Saami estimate (1/3) and that of the following study (22%), which is probably an artefact of the different range of samples used.

Population genetics of Finland revisited - looking Eastwards.

K. Rehnström et al.

We have previously reported that the genetic structure within Finland correlates well both with geography and known population history. While these studies have quantified the genetic distances between Finland and European neighbours to the south and the west, the influence of the Eastern and the Northern populations have not been described using genome-wide tools. Here we investigated the degree of Asian ancestry in Northern Europe. We also studied the genetic ancestry of geographic and linguistic neighbours of Finns, using genome-wide SNP data in a dataset comprising over 2200 individuals. First we quantied the proportions of European (represented by HapMap CEU) and Asian (HapMap CHB/JPT) genetic ancestry. Within Finland, the average Asian ancestry proportion varied from 2.5% in the Swedish speaking Finns to 5.1% in Northern Finland. The Saami population, being the indigenous inhabitants of Northern Finland, showed a surprisingly high proportion of Asian genetic ancestry (17.5%). We therefore hypothesize that, as genetic sharing between individuals in Northern Finland and Saami are higher than in other parts of the country, the Asian genetic ancestry in Finland could partly be through admixture with the Saami. Using a model-based estimation of individual ancestry, three ancestral populations provided a best fit for the combined Finnish and Saami dataset. Particularly, one of these ancestral populations was predominant in the Saami (average 78%), and higher in Northern Finland (average 14%) compared to the rest of the country (average 4%). Despite the fact that Finns are the closest relatives of the Saami of all populations included in this study, in general, our results show that language and genetics are only weakly related. The Finns are more closely related to most Indo-European speaking populations than to linguistically related populations such as the Saami. These analyses are currently being extended to sequence level variation using genome-wide sequence data for 100 Finns as part of the 1000 Genomes project, and 200 further individuals from the North-Eastern Finnish subisolate of Kuusamo. These 200 individuals provide good power to identify founder haplotypes within this isolate. Next, we aim to investigate the power to extend the imputation of haplotypes to the rest of Northern Finland as well as to the rest of the country.

It is unfortunate that these researchers used HapMap populations to study admixture in Finns; the Chinese are, especially, not a very good proxy for the East Eurasian element in the Finnish population. There are much data available on North Eurasian populations at this point, so I find the continued use of HapMap populations puzzling; hopefully this will be remedied when this research finds itself in the journals.

The current Dodecad estimate of East Eurasian admixture in the 1000 Genomes FIN population is 5.9%, the bulk of which is "Northeast Asian", a component which peaks in Nganasan, Chukchi, and Koryak, and is also well-represented in Central Siberia among Selkups. I don't have 5 Swedish-speaking Finns to report an average yet, but the ones I have are in the ~2-4% "Northeast Asian" range.

I also ran a quick test of FIN together with CEU and CHB and ~186k SNPs I am currently considering for the next version Dodecad v4 of my ancestry analysis. At K=2, FIN is 3.7% Asian, which seems consistent with the authors reporting the highest Asian ancestry of 5.1% in northern Finland, and also shows how the use of CHB as an Asian reference underestimates the degree of Eastern Eurasian admixture.

The impact of modern migrations on present-day multi-ethnic Argentina as recorded on the mitochondrial DNA genome

Maria LAURA Catelli et al.

Abstract (provisional)

Background
The genetic background of Argentineans is a mosaic of different continental ancestries. From colonial to present times, the genetic contribution of Europeans and sub-Saharan Africans has superposed to or replaced the indigenous genetic 'stratum'. A sample of 384 individuals representing different Argentinean provinces was collected and genotyped for the first and the second mitochondrial DNA (mtDNA) hypervariable regions, and selectively genotyped for mtDNA SNPs. This data was analyzed together with additional 440 profiles from rural and urban populations plus 304 from Native American Argentineans, all available from the literature. A worldwide database was used for phylogeographic inferences, inter-population comparisons, and admixture analysis. Samples identified as belonging to hg (hg) H2a5 were sequenced for the entire mtDNA genome.

Results
Phylogenetic and admixture analyses indicate that only half of the Native American component in urban Argentineans might be attributed to the legacy of extinct ancestral Argentineans and that the Spanish genetic contribution is slightly higher than the Italian one. Entire H2a5 genomes linked these Argentinean mtDNAs to the Basque Country and improved the phylogeny of this Basque autochthonous clade. The fingerprint of African slaves in urban Argentinean mtDNAs was low and it can be phylogeographically attributed predominantly to western African. The European component is significantly more prevalent in the Buenos Aires province, the main gate of entrance for Atlantic immigration to Argentina, while the Native American component is larger in North and South Argentina. AMOVA, Principal Component Analysis and hgs/haplotype patterns in Argentina revealed an important level of genetic sub-structure in the country.

Conclusions
Studies aimed to compare mtDNA frequency profiles from different Argentinean geographical regions (e.g., forensic and case-control studies) should take into account the important genetic heterogeneity of the country in order to prevent false positive claims of association in disease studies or inadequate evaluation of forensic evidence.

Shape of CEO's Face Linked to Company PerformanceThe shape of a CEO's face can predict his company's financial performance, according to a new study in which researchers analyzed photos of 55 male chief executive officers of Fortune 500 businesses.

The crucial feature: Facial width. Corporate leaders with faces that were wide relative to their length — such as Herb Kelleher, the former CEO of Southwest Airlines — tended to lead better-performing companies than CEOs with narrower faces, such as Dick Fuld, the long-faced final CEO of Lehman Brothers, the study found.

Wide faces in men have been linked with aggression and perceptions of untrustworthiness. Now researchers have discovered that broad-faced men appear more likely to deceive their counterparts in negotiations and are more willing to cheat in order to increase their financial gain.

I will add the CEO study abstract when I see it on the journal website (post a link in the comments if you've found it).

These results certainly go against the "don't judge a book by its cover" adage, and may mean that the old physiognomists from Pseudo-Aristotle to Lavater may have been onto something. I don't know what, if anything, they had to say about broad faces in particular, but it is certainly the case that the easy dismissal of their work in more recent times may have been premature.

Of course much of what was in the old physiognomy may have been the result of personal preferences/prejudices/experiences. Thankfully, nowadays we can evaluate stereotypes statistically to see whether they contain a grain of truth, and even discover novel associations.

I've always thought that there is an element of truth to physiognomy, judging from the visual and theatrical arts: heroes, villains, comical characters, princesses and evil witches are so often presented with distinctive visual cues that their presentation must touch on some objective anthropometric-behavioral reality.

Researchers spanning many scientific domains, including primatology, evolutionary biology and psychology, have sought to establish an evolutionary basis for morality. While researchers have identified social and cognitive adaptations that support ethical behaviour, a consensus has emerged that genetically determined physical traits are not reliable signals of unethical intentions or actions. Challenging this view, we show that genetically determined physical traits can serve as reliable predictors of unethical behaviour if they are also associated with positive signals in intersex and intrasex selection. Specifically, we identify a key physical attribute, the facial width-to-height ratio, which predicts unethical behaviour in men. Across two studies, we demonstrate that men with wider faces (relative to facial height) are more likely to explicitly deceive their counterparts in a negotiation, and are more willing to cheat in order to increase their financial gain. Importantly, we provide evidence that the link between facial metrics and unethical behaviour is mediated by a psychological sense of power. Our results demonstrate that static physical attributes can indeed serve as reliable cues of immoral action, and provide additional support for the view that evolutionary forces shape ethical judgement and behaviour.

August 29, 2011

A new technique which dates obsidian -- volcanic glass which can be fashioned into tools -- suggests that people were mining for obsidian in Mediterranean waters and shipping the once valuable rocks from the island of Melos in modern day Greece as far back as 15,000 years ago.
"Obsidian was a precious natural rock-glass found only in Melos, some in [the modern-day Greek areas of] Antiparos and Yali," explained Nicolaos Laskaris of the University of the Aegean in Greece. "From there it was spread all over the Aegean and in the continent too through contacts of trade."

If you wanted to have sharp tools and weapons in the days before bronze, you needed places like Melos. But you also needed a boat to get there. The evidence that people were crossing over to Melos even before the end of the last ice age comes from obsidian artifacts found in the Franchthi cave on the Peloponnese peninsula in southern mainland Greece -- far from the island of Melos. Previous geochemical work had already established the artifacts were from Melos, but figuring out when they were brought from the island is a trickier problem.

"They were sailors, certainly, especially in the Aegean region they followed little islands jumping like a frog reaching also Asia Minor and the Greek mainland," said Laskaris, who with his colleagues has published a paper about the discovery in the Sept. 2011 issue of Journal of Archaeological Science. "Until now only in Franchthi cave obsidians had been found at circa 8,500 B.C. Now we prove earlier contact with coastal sites was a fact."

Late Pleistocene/Early Holocene seafaring in the Aegean: new obsidian hydration dates with the SIMS-SS method

N. Laskaris, A. Sampson, F. Mavridis and I. Liritzis

AbstractArchaeological evidence regarding the presence of obsidian in levels that antedate the food production stage could have been the result of usage or intrusion of small obsidian artifacts from overlying Neolithic layers. The new obsidian hydration dates presented below employing the novel SIMS-SS method, offers new results of absolute dating concordant with the excavation data. Our contribution sheds new light on the Late Pleistocene/Early Holocene exploitation of obsidian sources on the island of Melos in the Cyclades reporting dates c. 13th millennium - end of 10th millennium B.P.

August 27, 2011

I calculated the Y-STR variance of the Busby et al. (2011) dataset, for both the 10 and 15 Y-STR sets, as well as 4- and 5-most "linear" subsets thereof. Generation length of 31.5 years is used for the calendar year estimates.

My position that Y-STRs are effectively dead for age estimation stands, but I thought it'd be a good exercise to do this, as my personal adieu to more than a decade of Y-STRs: they didn't live up to their promise, but, indirectly, they helped create an entire field of "genetic prehistory" that will live on after their demise.

The greatest contribution of the Busby et al. (2011) paper is that it has cured the naivete of some who bought into the "more STRs = more accuracy" scheme. After this paper all Y-STR based estimates (including my own, above) are suspect.

The non-linearity of the Y-STR mutation model is only one of the problems of Y-STRs. Over the last few years, I've examined many commonly held wrong assumptions about the way Y-STRs have been used:

The lack of appreciation of the true confidence intervals of age estimates (even under a well-behaved, symmetric stepwise mutation model), which are wider than believed by many, once uncertainty about generation length, mutation rates, and the inherent stochasticity of the mutation process is taken into account

A common conflation of haplogroup ages with migration events; a migration event may be actually much older or much younger than the Y-STR variance age, usually the latter, except in rare cases of the colonization of islands or remote regions of the world.

Influence of foreigner contamination or relics in the estimation of population ages.

From now on I am going on a Y-STR boycott on this blog. Y-STRs still have their obvious uses, for recent genealogy, or forensics. They may also convey some information about human prehistory in the broadest time scales.

But, on the whole, they are worse than useless for the prehistorian: not only do they produce estimates fraught with danger, but also, being the only game in town, are prone to over-interpretation and spurious associations.

Thankfully, it will only be a few years more until we can move past the Y-STR swamp, and into the more promising territory of well-behaved unique event polymorphisms that are currently too costly to type on a large number of samples. Archaeogenetics will also help, although that, too, has its own perils (namely contamination, and the inability to get data from the hot and humid regions of the world).

One way or another, we're bound to know more in the future, and destroying the Y-STR behemoth is the first step toward making some real progress in genetic prehistory.

August 25, 2011

Link to supplement (pdf). I haven't read the paper yet, but this bit from a story on it seems to gel well with my Palaeoafrican admixture theory:

While Europe and Asia might now be viewed as a hotbed of interbreeding, modern humans who stayed in Africa appear to have been active interbreeders as well. Neanderthals and Denisovans weren't present, but other archaic human groups likely were.

"Well established is that modern Africans have greater genetic diversity, overall, than the modern populations of other continents," Parham said. "This greater diversity is likely due to what was inherited from earlier forms of Homo, combined with interbreeding between different forms of Homo."

The early ancestors of all modern people, then, did not seem to shy away from breeding with different human species, actions that strengthened our immune systems and likely resulted in other benefits yet to be revealed.

It seems that multiregional evolution isn't dead, after all, as I suggested recently, and the explicit use of the word "multiregional" in the paper's title is probably indicative of the shifting atmosphere.

The Shaping of Modern Human Immune Systems by Multiregional Admixture with Archaic Humans

Laurent Abi-Rached et al.

ABSTRACT

Whole-genome comparisons identified introgression from archaic to modern humans. Our analysis of highly polymorphic HLA class I, vital immune system components subject to strong balancing selection, shows how modern humans acquired the HLA-B*73 allele in west Asia through admixture with archaic humans called Denisovans, a likely sister group to the Neandertals.Virtual genotyping of Denisovan and Neandertal genomes identified archaic HLA haplotypes carrying functionally distinctive alleles that have introgressed into modern Eurasian and Oceanian populations. These alleles, of which several encode unique or strong ligands for natural killer cell receptors, now represent more than half the HLA alleles of modern Eurasians and also appear to have been later introduced into Africans. Thus, adaptive introgression of archaic alleles has significantly shaped modern human immune systems.

I've been quite skeptical of the interpretation of the published Neandertal genome as evidence for Neandertal admixture in Eurasians. Of course, such admixture is a possibility, but I remain unconvinced that the Neandertal admixture thesis has managed to shoulder out other interpretations.

A new paper shows how the mtDNA evidence is inconsistent with Neandertal admixture, by looking at ancient Homo sapiens, Neandertal, and modern human mtDNA. The basic idea is simple, that if admixture with Neandertals did take place at the levels predicted (~4%), then we would expected to see some Neandertal-like mtDNA in either ancient or modern humans, but we don't.

There are some alternative explanations for the lack of Neandertal-like mtDNA in modern humans that I have considered:

Modern human-Neandertal crossings were female-male exclusively.

Neandertal mtDNA sequences were weeded out by natural selection, perhaps because Neandertal mtDNA was well-adapted to extreme cold and became maladaptive in modern human bodies, as the latter had better cold-protection technology (tight clothes, for example), and the glaciers retreated anyway.

I can entertain #1, although it's often the case the the group that has the upper hand often mates with the females of the disadvantaged group, and not vice versa. In any case, I don't see any evidence for it, and the lack of archaic-like Y-chromosomes in Eurasians is probably inconsistent with it.

I had a certain degree of appreciation for #2 until recently. If Europeans had Neandertal admixture, and Neandertal mtDNA was maladaptive to a postglacial technological environment, then selection is a reasonable hypothesis.

However, if Neandertal admixture affected all Eurasians equally, as the current theory holds, then there are plenty of people in North Asia that continued to live in glacial-like temperatures and with predominantly meat diets until the present. Why would Neandertal mtDNA be maladaptive in them?

At present I retain my agnosticism on the subject of Neandertal admxture: the Neandertal genome studies have certainly proven one thing: that archaic humans are not irrelevant to the human story. How they are relevant remains to be seen.

AJPA DOI: 10.1002/ajpa.21569

No evidence of Neandertal admixture in the mitochondrial genomes of early European modern humans and contemporary Europeans

Silvia Ghirotto et al.

Neandertals, the archaic human form documented in Eurasia until 29,000 years ago, share no mitochondrial haplotype with modern Europeans. Whether this means that the two groups were reproductively isolated is controversial, and indeed nuclear data have been interpreted as suggesting that they admixed. We explored the range of demographic parameters that may have generated the observed mitochondrial diversity, simulating 3.0 million genealogies under six models differing as for the relationships among contemporary Europeans, Neandertals, and Upper Palaeolithic European early modern humans (EEMH), who coexisted with Neandertals for millennia. We compared by Approximate Bayesian Computations the simulation results with mitochondrial diversity in 7 Neandertals, 3 EEMH, and 150 opportunely chosen modern Europeans.A model of genealogical continuity between EEMH and contemporary Europeans, with no Neandertal contribution, received overwhelming support from the analyses. The maximum degree of Neandertal admixture, under the model of gene flow supported by nuclear data, was estimated at 1.5%, but this model proved 20–32 times less likely than a model without any gene flow. Nuclear and mitochondrial evidence might be reconciled if smaller population sizes led to faster lineage sorting for mitochondrial DNA, and Neandertals shared a longer period of common ancestry with the non-African's than with the African's ancestors.

Saudi officials say archaeologists have begun excavating a site that suggests horses were domesticated 9,000 years ago in the Arabian Peninsula.

The vice-president of the Saudi Commission for Tourism and Antiquities said the discovery at al-Maqar challenged the theory it first took place 5,500 years ago in Central Asia.

Ali al-Ghabban said it also changed what was known about the evolution of culture in the late Neolithic period.

A number of artefacts were also found.

They included arrowheads, scrapers, grain grinders, tools for spinning and weaving, and other tools that showed the inhabitants were skilled at handicrafts.

Mr Ghabban said carbon-14 tests on the artefacts, as well as DNA tests on human remains also found there, dated them to about 7,000 BC.

"This discovery will change our knowledge concerning the domestication of horses and the evolution of culture in the late Neolithic period," he told a news conference in Jeddah, according to the Reuters news agency.

"The al-Maqar civilisation is a very advanced civilization of the Neolithic period. This site shows us clearly, the roots of the domestication of horses 9,000 years ago," he added.

Although humans came into contact with horses about 50,000 years ago, they were originally herded for meat, skins, and possibly for milk.

The first undisputed evidence for their domestication dates back to 2,000 BC, when horses were buried with chariots. By 1,000 BC, domestication had spread through Europe, Asia and North Africa.

However, researchers have found evidence suggesting that the animals were used by the Botai culture in northern Kazakhstan 5,500 years ago.

August 24, 2011

I will probably update this entry when I read the actual paper carefully.

Nonetheless, it seems to confirm that the marker set influence on TMRCA estimates that Tim Janzen reported and I highlighted is a nuissance even for a relatively young haplogroup. It is also probably consistent with the idea that Y-STR based estimates are suspect because of deviations from the linear model.

UPDATE I (An epitaph for Y-STRs)

The paper could just as easily have been titled "An epitaph for Y-STRs". Of course, Y-STRs do carry information related to antiquity; and there are so many datasets collected from both academics and genealogist enthusiasts. Thus, they will continue to be used and analyzed for at least a few years more.

Nonetheless, the conclusion is inescepable that a very specific use of Y-STRs on modern populations, with the goal of discovering tight links with archaeological/historical events is all but dead.

The reason is simple: as clocks, they suck. A bad clock is not useless: it gives you some information about time. Moreover, you can often use several to iron out the inaccuracy of any single one of them.

Unfortunately, better estimation through averaging of bad estimators works only in one case: when the estimators are unbiased.

An unbiased estimator has an expected value equal to what you are trying to estimate. For example, suppose that the true age of a founder is 100 generations. For various reasons, bad clocks may give you estimates different than 100: some more, some less.

But, if some of them tend to give you an estimate of around 50 generations, and some of them tend to give you estimates around 200 generations, then averaging them out tells you nothing, except what ratio of slow and fast clocks you used.

Use more fast ones, and get a recent estimate; use more slow ones and get a more ancient one. Here is a figure from the paper, showing age estimates of sub-haplogroups R-S21 vs. R-S116:

The different codes are explained in the supplementary material, but notice the difference between 4.A (the 4 most "linear") and 4.C (the 4 least "linear"). Using a generation length of 31.5 years, these correspond to 8.3ky BP and 2.4ky BP, i.e., a >3-fold difference.

Using "all" 15 Y-STRs (15.all) leads to an age of 3.4ky BP, but the analysis of Busby et al. show how misleading this is: using all 15 Y-STRs is simply averaging out a set of bad clocks: the 3.4ky BP is not dominated by the actual split between the two haplogroups, but is actually an artefact of the set of clocks used.

Here is Table 1 from the paper, notice the last column:

The last column is an estimate of the duration of linearity for a Y-STR. It is basically an estimate (in years) of the time span during which a Y-STR accumulates variance in a predictable (linear) manner, which can be calculated from a combination of the range of the Y-STR (the possible values it can take), and its mutation rate (how often it changes its value).

The basic idea is simple: a big room (great range) allows more freedom of movement before you hit one of the walls; a fly (high mutation rate) is more likely to hit a wall before a tortoise.

A Y-STR with a small range and a high mutation rate is hopeless because its propensity to change its value (high mutation rate) is checked by its smaller range.

Going back to the table, we see that many Y-STRs have linearity durations lower than the middle of the Bronze Age, and some of them much lower. This means that including these Y-STRs will tend to suppress age estimates to make them appear younger.

(to be continued)

UPDATE II: Lack of cline in Europe

The authors showed that the observed east-west clinality of Y-STR variance from Turkey to the Atlantic was spurious and there is no longer any longitudinal pattern of decreasing variation. I made exactly the same point in January 2010, when Balaresque et al. appeared:

Equally flawed is the inference that R1b1b2 is clinal (Figure 2A). Microsatellite variance is not significantly higher in Turkey than in Europe -- even if one makes the questionable assumption that modern Anatolian Turks are patrilineal descendants of Neolithic Anatolians. The significance of the regression line disappears if 1 or 2 data points are excluded, and the plot has a quite visible "gap" between Turkey and Italy corresponding to the entirety of eastern Europe and the Balkans, i.e. the routes that any putative Neolithic lineages would have entered Europe

The authors of the current paper seem to be agnostic as to when R-M269 arrived in Europe. As Dr. Capelli says in an otherwise sensationalist BBC piece:

"At the moment it's not possible to claim anything about the age of this lineage," he told BBC News, "I would say that we are putting the ball back in the middle of the field."

In the actual paper, the lack of an east-west cline is interpreted as inconsistent with the Neolithic model:

the homogeneity of STR variance and distribution of sub-types across the continent are inconsistent with the hypothesis of the Neolithic diffusion of the R-M269 Y chromosome lineage.

Personally, I've often emphasized the huge (underappreciated) confidence intervals associated with Y-STR based estimates, so I appreciate the "caution" part of the paper. I was reading the Haplogroup R page on ISOGG, and the statement...

Haplogroup R1b1a2-M269 is observed most frequently in Europe, especially western Europe, but with notable frequency in southwest Asia. R1b1a2-M269 is estimated to have arisen approximately 4,000 to 8,000 years ago in southwest Asia and to have spread into Europe from there.

... pretty much sums up my views on the subject, although I would add that I consider the most likely place of origin of R-M269 to be in the highlands west and south of the Caspian sea, "complementary" to an early R-M17 distribution in the arc of flatlands north and east of the Caspian.

I think that there are many possible migration routes and possible archaeological correlates of the R-M269 spread, but at the moment, a Neolithic-to-Bronze age dispersal is the more likely hypothesis. Indeed, the Paleolithic hypothesis cannot be saved even with the recognition of the phenomena described in this paper, since, as we have seen even the most "linear" markers produce an 8.3ky BP age. Only a descent to the murky territory of the evolutionary rate can save that hypothesis.

What about the lack of clinality across Europe? A point that is overlooked, I think is that clinality does not necessarily follow from a geographical range expansion. Two additional conditions must hold:

The dispersal must be slow, so that variation begins to accumulate at very different dates at the near and far ends of the expansion range

The number of founder colonists spreading at any stage of the expansion must be very low, otherwise they will carry pretty much all the diversity found in their parent population.

The classic demic diffusion model is dead, so I don't particularly see why would expect to see a cline in Europe in either the case of small pioneer expeditions or folk migrations.

Proc. R. Soc. B doi: 10.1098/rspb.2011.1044

The peopling of Europe and the cautionary tale of Y chromosome lineage R-M269

George B. J. Busby et al.

Recently, the debate on the origins of the major European Y chromosome haplogroup R1b1b2-M269 has reignited, and opinion has moved away from Palaeolithic origins to the notion of a younger Neolithic spread of these chromosomes from the Near East. Here, we address this debate by investigating frequency patterns and diversity in the largest collection of R1b1b2-M269 chromosomes yet assembled. Our analysis reveals no geographical trends in diversity, in contradiction to expectation under the Neolithic hypothesis, and suggests an alternative explanation for the apparent cline in diversity recently described. We further investigate the young, STR-based time to the most recent common ancestor estimates proposed so far for R-M269-related lineages and find evidence for an appreciable effect of microsatellite choice on age estimates. As a consequence, the existing data and tools are insufficient to make credible estimates for the age of this haplogroup, and conclusions about the timing of its origin and dispersal should be viewed with a large degree of caution.

August 23, 2011

The sequenced horses can be found in the supplement, and they all seem to be from Alaska/Yukon/Siberia, probably for reasons having to with DNA preservation.

Hopefully techniques will improve, and the study of ancient wild horse DNA may help identify the wild progenitors of domestic horses, which must have lived in the more western parts of Eurasia, rather than in the studied regions.

With domesticated crops we have been fortunate in still having access to their wild relatives, but wild horses are now all extinct, except Przewalski's horse, which, as as other research has also shown was not the progenitor of domesticated horses.

Discovery of lost diversity of paternal horse lineages using ancient DNA

Sebastian Lippold et al.

Abstract

Modern domestic horses display abundant genetic diversity within female-inherited mitochondrial DNA, but practically no sequence diversity on the male-inherited Y chromosome. Several hypotheses have been proposed to explain this discrepancy, but can only be tested through knowledge of the diversity in both the ancestral (pre-domestication) maternal and paternal lineages. As wild horses are practically extinct, ancient DNA studies offer the only means to assess this ancestral diversity. Here we show considerable ancestral diversity in ancient male horses by sequencing 4 kb of Y chromosomal DNA from eight ancient wild horses and one 2,800-year-old domesticated horse. Both ancient and modern domestic horses form a separate branch from the ancient wild horses, with the Przewalski horse at its base. Our methodology establishes the feasibility of re-sequencing long ancient nuclear DNA fragments and demonstrates the power of ancient Y chromosome DNA sequence data to provide insights into the evolutionary history of populations.

Abstract
BACKGROUND:
Blue eyes have been the embodiment of attractiveness not only for decades but even for centuries. The primary aim of this study was to determine whether iridal color, particularly color blue, can increase the attractiveness of a person's eye area. As a secondary aim, the study examined the impact of pupil diameter and scleral color on the attractiveness of the eye area.

METHODS:The stimulus material comprised images of the eye areas of 60 women ages 15-65 years. A total of 80 participants rated the attractiveness of each eye area on a 7-point Likert scale and estimated the age of the person. The color values of the iris and sclera were measured. As an additional subsample, 50% of the participants were asked what features of each eye area they found particularly appealing.

RESULTS:Most surprisingly, no correlation was found between iridal color and rated attractiveness. However, the participants mentioned the color blue more often as a positive aspect than other iridal colors. A high inverse correlation was observed between attractiveness of the eye area and age. The larger the pupil diameter and the whiter the scleral color, the lower was the real and perceived age and the higher was the attractiveness.

CONCLUSION:The data showed that the "blue-eyes stereotype" does exist. People consider blue eyes attractive, but in reality, blue is rated as attractive as other iridal colors. Bright scleral color and large pupils positively affect attractiveness because both features are significantly correlated with youthfulness.

August 22, 2011

Tunisia has experienced a variety of human migrations that have modeled the myriad cultural groups inhabiting the area. Both Arabic and Berber-speaking populations live in Tunisia. Berbers are commonly considered as in situ descendants of peoples who settled roughly in Palaeolithic times, and posterior demographic events such as the arrival of the Neolithic, the Arab migrations, and the expulsion of the “Moors” from Spain, had a strong cultural influence. Nonetheless, the genetic structure and the population relationships of the ethnic groups living in Tunisia have been poorly assessed. In order to gain insight into the paternal genetic landscape and population structure, more than 40 Y-chromosome single nucleotide polymorphisms and 17 short tandem repeats were analyzed in five Tunisian ethnic groups (three Berber-speaking isolates, one Andalusian, and one Cosmopolitan Arab). The most common lineage was the North African haplogroup E-M81 (71%), being fixed in two Berber samples (Chenini–Douiret and Jradou), suggesting isolation and genetic drift. Differential levels of paternal gene flow from the Near East were detected in the Tunisian samples (J-M267 lineage over 30%); however, no major sub-Saharan African or European influence was found. This result contrasts with the high amount of sub-Saharan and Eurasian maternal lineages previously described in Tunisia. Overall, our results reveal a certain genetic inter-population diversity, especially among Berber groups, and sexual asymmetry, paternal lineages being mostly of autochthonous origin. In addition, Andalusians, who are supposed to be migrants from southern Spain, do not exhibit any substantial contribution of European lineages, suggesting a North African origin for this ethnic group.

Mitochondrial DNA (mtDNA) and Y-chromosome variation has been studied in Bou Omrane and Bou Saâd, two Tunisian Berber populations. In spite of their close geographic proximity, genetic distances between them were high and significant with both uniparental markers. A global analysis, including all previously studied Tunisian samples, confirmed the existence of a high female and male population structure in this country. Analyses of molecular variance analysis evidenced that this differentiation was not attributable to ethnic differences. Mantel test showed that, in all cases, Y-chromosome haplotypic distances correlated poorly with geography, whereas after excluding the more isolated samples of Bou Omrane and Bou Saâd, the mtDNA pattern of variation is significantly correlated with geography. Congruently, the Nm ratio of males versus females pointed to a significant excess of female migration rate across localities, which could be explained by patrilocality, a common marriage system in rural Tunisia. In addition, it has been observed that cultural isolation in rural communities promotes, by the effect of genetic drift, stronger loss of diversity and larger genetic differentiation levels than those observed in urban areas as deduced from comparisons of their respective mean genetic diversity and their respective mean genetic distances among populations. It is likely that the permanent exodus from rural to urban areas will have important repercussions in the future genetic structure of this country.

August 20, 2011

In summary, careful error analysis led us to believe that the differences in the mutation rate observed between the different population sample groups are likely to result from biological processes, rather than measurement or analytical artifacts.

A Comprehensive Map of Mobile Element Insertion Polymorphisms in Humans

Chip Stewart et al.

As a consequence of the accumulation of insertion events over evolutionary time, mobile elements now comprise nearly half of the human genome. The Alu, L1, and SVA mobile element families are still duplicating, generating variation between individual genomes. Mobile element insertions (MEI) have been identified as causes for genetic diseases, including hemophilia, neurofibromatosis, and various cancers. Here we present a comprehensive map of 7,380 MEI polymorphisms from the 1000 Genomes Project whole-genome sequencing data of 185 samples in three major populations detected with two detection methods. This catalog enables us to systematically study mutation rates, population segregation, genomic distribution, and functional properties of MEI polymorphisms and to compare MEI to SNP variation from the same individuals. Population allele frequencies of MEI and SNPs are described, broadly, by the same neutral ancestral processes despite vastly different mutation mechanisms and rates, except in coding regions where MEI are virtually absent, presumably due to strong negative selection. A direct comparison of MEI and SNP diversity levels suggests a differential mobile element insertion rate among populations.

We describe the saliva microbiome diversity in Batwa Pygmies, a former hunter-gatherer group from Uganda, using next-generation sequencing of partial 16S rRNA sequences. Microbial community diversity in the Batwa is significantly higher than in agricultural groups from Sierra Leone and the Democratic Republic of Congo. We found 40 microbial genera in the Batwa, which have previously not been described in the human oral cavity. The distinctive composition of the salvia microbiome of the Batwa may have been influenced by their recent different lifestyle and diet.

August 16, 2011

Razib has an interesting post in which he argues that as living conditions become good for most members of a society, the environmental component of intelligence should diminish, and the genetic one should increase.

The basic idea could be expressed as follows: give the exact same amount of water, sunlight, nutrients, etc. to two different trees, and the amount of fruit they will produce will depend entirely on their genes.

Likewise, make sure every kid has food, clean water, a home, medical care, schooling, etc. and then their differences in intelligence will depend entirely on their genes.

Hence:

A perfect meritocracy would replace cultural class with biological caste.

It's a seductive argument, that overlooks, I think, an important factor:

Different organisms have different optimal environments for their best performance.

Let's go back to the tree analogy. If you equalize their environments, then their output (fruit) will depend entirely on their genetic input (genes). But what environment should be chosen?

A desert plant is ruined by too much water, a jungle one by too little.

It is far from an obvious proposition that the "ideal environment" as currently envisioned by Western social policy makers is indeed the optimal one for all members of our species.

A Norwegian and a Nigerian will both suffer if they are exposed to the sun too much or too little, but their optimal "sun exposure" points are different; a Pygmy and an Eskimo will die of starvation with too little food and of a variety of ailments with too much, but their optimal "daily colorie intake" points are different. Even members of the same population differ in what is good for them.

In Aristotelian terminology, "mean is best", but "mean" is not the same for all, and what is an excess for one is a deficiency for another.

It could be argued that current affluent societies do not enforce particular environments, but give the freedom to their members to choose their own. In a truly affluent society where anyone has the means to adopt whatever lifestyle is best for them, it will be the case that variation in any particular trait (e.g., intelligence) will depend on one's genes: Norwegians, Nigerians, Pygmies, and Eskimos may choose what is good for them, they are not forced to live in a suboptimal environment

That, however, is a mixed blessing because a free society is also a very particular kind of society that is not necessarily best for all. It could very well be that some organisms reach their optimum performance under compulsion, and I see no reason to think that kids (or adults) become excellent by doing what they want and not by following the instructions of those who know better.

For example, kids learn to read and do multiplications by being forced to do a lot of tedious repetition. In a free society, an adult is largely free from compulsion, but that does not mean that he will choose to do what is best for himself.

In a free and affluent society everyone has the potential of having the best possible physique and the best possible cognitive ability that their genotype will allow: "money is no object." But, as we well know, few people use their freedom to achieve their full potential.

In conclusion:

Fix the genes (as in clones or identical twins) and all variation is due to the environment

Fix the environment and all variation is due to genes

The eugenicist's dream is to "improve the genes" -- but "better genes" for what environment?

The social engineer's dream is to "improve the environment" -- but "better environment" for which genetic natures?

August 12, 2011

It is unfortunate that what seems to be a good sized sample of regional Armenian sample was only analyzed with a small set of autosomal STRs. Hopefully, the sample may still be available in the future for more comprehensive tests.

Population codes can be found in a freely available supplementary table.

I had previously used a similar set of STRs with structure to estimate inter-continental admixture in a set of "pure", and widely differentiated individuals (Germans, Africans, Chinese). That suggested to me, that while the continent origin can indeed be guessed for most individuals, admixture proportions are extremely noisy. For much closer-related populations (Armenian groups and various other Caucasoid neighbors), I fear that we should be extremely cautious in over-interpreting the limited evidence that a small panel of STRs provides.

Here are also Dodecad v3 population portraits for the Behar et al. (2010) Armenian sample and the Armenian_D sample from the Dodecad project:

I do not have enough Armenian participants yet, to speak about possible substructure in that population, but, from the samples available so far, which are from several different regions, a picture of relative homogeneity emerges. I encourage individuals with 4 Armenian grandparents who've tested with either 23andMe or Family Finder to join the Project (send e-mail to dodecad@gmail.com).

AbstractThe archeology and ethnology of Armenia suggest that this region has acted as a crossroads for human migrations from Europe and the Middle East since at least the Neolithic. Near continual foreign influx has, in turn, led to the supposition that the gene pools of geographically separated Armenian populations may have diverged as differing historical influences potentially left distinct genetic traces in the various regions of the Armenian plateau. In this study, we seek to address whether any evidence for such genetic regional partitioning in Armenians exists by analyzing, for the first time, 15 autosomal short tandem repeat (STR) loci in 404 Armenians from four geographically well-characterized collections (Ararat Valley, Gardman, Sasun, and Lake Van) that represent distinct communities from across Historical Armenia. In addition, to determine whether genetic differences among these four Armenian populations are the result of differential affinities to populations of known historical influence in Armenia, we utilize 27 biogeographically targeted reference populations for phylogenetic and admixture analyses. From these examinations, we find that while close genetic affiliations exist between the two easternmost Armenian groups analyzed, Ararat Valley and Gardman, the remaining two populations display substantial distinctions. In particular, Sasun is distinguished by evidence for genetic contributions from Turkey, while a stronger Balkan component is detected in Lake Van, potentially suggestive of remnant genetic influences from ancient Greek and Phrygian populations in this region.

August 10, 2011

Cornwall, Devon and Pembrokeshire were pooled to represent the South/West (SW) and the area that could be considered the closest surrogate to the Ancient British. Kent, Norfolk and Lincolnshire were pooled to represent the East (E) and the area most directly influenced by the Anglo-Saxon invasions. Cumbria, Yorkshire and the North East were pooled broadly to represent the North of England (N); Oxfordshire and the Forest of Dean were combined to represent the Central region of England (CN); and Orkney was kept separate from the others, largely because of the known substantial Norse Viking influence in Orkney.

Of interest are the NRY haplogroup data:

The SW seems to have the lowest R1a1 frequency (1.3%). This is in agreement with the Dodecad v3 results for Cornwall (1.8% East European). The E seems to have an intermediate frequency (3.5%), again in agreement with Dodecad v3 for Kent (3.7%). Orkney has the highest R1a1 frequency (34.2%) and also the highest East European component in Dodecad v3 (11%). So, it does seem that R1a1 frequency tracks an eastern population element in the British isles.

R1xR1a1 has its lowest values in E and OR; this is probably consistent with the idea that Germanic invaders from the east possessed less of this haplogroup than the pre-Germanic population.

The minor alleles in MC1R are associated with red hair, and it seems that this is maximized in Orkney.

The admixture estimates are also quite interesting, showing a dependence on the use of local (L) vs. non-local (N) surnames; the results do suggest non-trivial shifts in genetic composition since the adoption of surnames.

People of the British Isles: preliminary analysis of genotypes and surnames in a UK-control population

Bruce Winney et al.

There is a great deal of interest in a fine-scale population structure in the UK, both as a signature of historical immigration events and because of the effect population structure may have on disease association studies. Although population structure appears to have a minor impact on the current generation of genome-wide association studies, it is likely to have a significant part in the next generation of studies designed to search for rare variants. A powerful way of detecting such structure is to control and document carefully the provenance of the samples involved. In this study, we describe the collection of a cohort of rural UK samples (The People of the British Isles), aimed at providing a well-characterised UK-control population that can be used as a resource by the research community, as well as providing a fine-scale genetic information on the British population. So far, some 4000 samples have been collected, the majority of which fit the criteria of coming from a rural area and having all four grandparents from approximately the same area. Analysis of the first 3865 samples that have been geocoded indicates that 75% have a mean distance between grandparental places of birth of 37.3 km, and that about 70% of grandparental places of birth can be classed as rural. Preliminary genotyping of 1057 samples demonstrates the value of these samples for investigating a fine-scale population structure within the UK, and shows how this can be enhanced by the use of surnames.

The endangered Przewalski’s horse is the closest relative of the domestic horse and is the only true wild horse species surviving today. The question of whether Przewalski’s horse is the direct progenitor of domestic horse has been hotly debated. Studies of DNA diversity within Przewalski’s horses have been sparse, but are urgently needed to ensure their successful reintroduction to the wild. In an attempt to resolve the
controversy surrounding the phylogenetic position and genetic diversity of Przewalski’s horses, we used massively parallel sequencing technology to decipher the complete mitochondrial and partial nuclear genomes for all four surviving maternal lineages of Przewalski’s horses. Unlike SNP typing usually affected by ascertainment bias, the present method is expected to be largely unbiased. Three mitochondrial haplotypes were discovered - two similar ones, haplotypes I/II, and one substantially divergent from the other two, haplotype III. Haplotypes I/II vs. III did not cluster together on a phylogenetic tree, rejecting the monophyly of Przewalski’s horse maternal lineages, and were estimated to split 0.117-0.186 million years ago, significantly preceding horse domestication. In the phylogeny based on autosomal sequences, Przewalski’s horses formed a monophyletic clade, separate from the Thoroughbred domestic horse lineage. Our results suggest that Przewalski’s horses have ancient origins and are not the direct progenitors of domestic horses. The analysis of the vast amount of sequence data presented here suggests that Przewalski’s and domestic horse lineages diverged at least 0.117 million years ago, but since then have retained ancestral genetic polymorphism and/or experienced gene flo

August 07, 2011

Genetic features of ancient West Siberian people of the Middle Ages, revealed by mitochondrial DNA haplogroup analysis.

Sato T, Razhev D, Amano T, Masuda R.

In order to investigate the genetic features of ancient West Siberian people of the Middle Ages, we studied ancient DNA from bone remains excavated from two archeological sites in West Siberia: Saigatinsky 6 (eighth to eleventh centuries) and Zeleny Yar (thirteenth century). Polymerase chain reaction amplification and nucleotide sequencing of mitochondrial DNA (mtDNA) succeeded for 9 of 67 specimens examined, and the sequences were assigned to mtDNA haplogroups B4, C4, G2, H and U.This distribution pattern of mtDNA haplogroups in medieval West Siberian people was similar to those previously reported in modern populations living in West Siberia, such as the Mansi, Ket and Nganasan. Exact tests of population differentiation showed no significant differences between the medieval people and modern populations in West Siberia. The findings suggest that some medieval West Siberian people analyzed in the present study are included in direct ancestral lineages of modern populations native to West Siberia.

August 05, 2011

Finally, we show by the application of kinship coefficients that the majority of rare CNVs are passing through germ-lines rather than being de novo variants, and therefore are heritable and provide an index of relatedness. The inheritance of CNVs could be observed in actual pedigrees, which confirmed the increased relatedness between CNV carriers. The similar relationship between genetic variants and kinship was observed in a study of the same population in Vis, which found kinship inferred from pedigree information was consistent with segregation of SNPs in the population [44].

PLoS ONE 6(8): e23087. doi:10.1371/journal.pone.0023087

Copy Number Variation across European Populations

Wanting Chen et al.

Genome analysis provides a powerful approach to test for evidence of genetic variation within and between geographical regions and local populations. Copy number variants which comprise insertions, deletions and duplications of genomic sequence provide one such convenient and informative source. Here, we investigate copy number variants from genome wide scans of single nucleotide polymorphisms in three European population isolates, the island of Vis in Croatia, the islands of Orkney in Scotland and the South Tyrol in Italy. We show that whereas the overall copy number variant frequencies are similar between populations, their distribution is highly specific to the population of origin, a finding which is supported by evidence for increased kinship correlation for specific copy number variants within populations.

Does anyone think this sort of scientific teasing serves any purpose? Or that science would not be better served if results were published immediately rather than go through the venerated but time consuming rituals of conference presentation, journal submission, peer review, publication?

Patterns of genetic diversity have previously been shown to mirror geography on a global scale and within continents and individual countries. Using genome-wide SNP data on 5174 Swedes with extensive geographical coverage, we analyzed the genetic structure of the Swedish population.We observed strong differences between the far northern counties and the remaining counties. The population of Dalarna county, in north middle Sweden, which borders southern Norway, also appears to differ markedly from other counties, possibly due to this county having more individuals with remote Finnish or Norwegian ancestry than other counties. An analysis of genetic differentiation (based on pairwise Fst) indicated that the population of Sweden's southernmost counties are genetically closer to the HapMap CEU samples of Northern European ancestry than to the populations of Sweden's northernmost counties. In a comparison of extended homozygous segments, we detected a clear divide between southern and northern Sweden with small differences between the southern counties and considerably more segments in northern Sweden. Both the increased degree of homozygosity in the north and the large genetic differences between the south and the north may have arisen due to a small population in the north and the vast geographical distances between towns and villages in the north, in contrast to the more densely settled southern parts of Sweden. Our findings have implications for future genome-wide association studies (GWAS) with respect to the matching of cases and controls and the need for within-county matching. We have shown that genetic differences within a single country may be substantial, even when viewed on a European scale. Thus, population stratification needs to be accounted for, even within a country like Sweden, which is often perceived to be relatively homogenous and a favourable resource for genetic mapping, otherwise inferences based on genetic data may lead to false conclusions.

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